Dear Nat,

     You are making an excellent point, that I would like to supplement with
another drawn from an intermediate stage between making compulsory the
deposition of coordinates (to which you are referring) and the discussion we
are having right now about moving towards the deposition of diffraction
images - namely, the deposition of "structure factor" data.

     At first that idea seemed to many to be just as far-fetched as the
current one is seen by many. I can remember an impassioned e-mail to this BB
by Gerard Kleywegt with subject line "SOS: save our structure factors!",
pleading the case for that deposition to be made cmpulsory so as to be make
it possible to have as objective a picture as possible of the quality of the
electron density on which the model was based; and he went on to produce the
Electron Density Server, the usefulness of which few would now dispute.
There are probably few instances in which the EDS could be proven to have
led to "significant new biological insights", but it is undeniable that it
must have provided very useful means of checking deposited structures to see
whether there might be questionable bits in crucial regions, whereas
previously one would have had to believe indiscriminately everything that
was modelled.

     This structure factor deposition also led to the possibility of
large-scale testing of new developments in refinement algorithms which
played a huge role in helping improvements in those to be throroughly
evaluated, and the programs to be made robust. This led in turn to being
able to see more detail or more corrections in old pdb entries via the EDS,
culminating in such initiatives as PDB-redo that, if not revolutionising the
biological information content of the pdb, has certainly helped make its
contents much more assessable. Through the effect on the improvement of
refinement programs, it can be said that the greatest beneficiaries of the
deposition of structure factors yesterday are not so much the people who
deposited the associated structures at the time, but everyone who refines
structures today and will do so tomorrow with the much improved programs it
has helped produce.

     We are simply today at the logical next step, i.e. depositing the
images that the structure factors came from. For many reasons that have been
described by many people, images often contain much more information about
the reliability (or otherwise) of the structure factors derived from them (I
have repeatedly mentioned the corruption by reflexions from parasitic
lattices). Such images will not only provide the foodstuff for new
developments aimed at dealing better with the problem: once those
developments have taken place, more reliable data will be obtainable from
them, that may frequently clean up dubious features of the previous maps or
bring into question certain parts of the previous models. I think that
Adrian's rather dismissive comment that developers can get the job done from
a few scraps of bad images gleaned from colleagues in distress is simply a
sign of a lack of experience in developing software.

     We should not, therefore, be too blinkered and ask only "What will it
do for my structure if I deposit my images", but instead ask "What will
depositing my images do to improve the processing and refinement programs of
tomorrow" (I am not trying to sound like JFK here ...). The answer is: an
awful lot! These improvements will then help everybody, including the
sceptical depositor in question in his or her next tough project; but as
usual they will be taken for granted by those who thought that depositing
images was a waste of time ... .

     I hope this elicits more comments from doubters and detractors: their
voices and arguments should certainly be heard.


     With best wishes,
     
          Gerard.

--
On Thu, Oct 27, 2011 at 02:11:28PM -0700, Nat Echols wrote:
> On Thu, Oct 27, 2011 at 1:47 PM, Adrian Goldman
> <[log in to unmask]>wrote:
>
> > 1) this is not a matter of science, but science (internal) policy, and so
> > the majority actually SHOULD count.
> >
>
> It's worth keeping in mind that there was once strong opposition to the
> current rules on PDB deposition - the best example I could find is here:
>
> http://www.nature.com/nsmb/journal/v5/n6/pdf/nsb0698-407.pdf
>
> Notably, nearly a third of scientists polled thought they should be allowed
> to publish without releasing coordinates. If this had been a majority,
> should the journal editors have meekly submitted and allowed the old policy
> of 1-year holds to continue? Admittedly, the issue of archiving raw images
> is not the same, since they are of much less use to the community, but it's
> a good example of why some opinions should be ignored.
>
> -Nat

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